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- PDB-1qjw: CEL6A (Y169F) WITH A NON-HYDROLYSABLE CELLOTETRAOSE -

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Basic information

Entry
Database: PDB / ID: 1qjw
TitleCEL6A (Y169F) WITH A NON-HYDROLYSABLE CELLOTETRAOSE
ComponentsCELLOBIOHYDROLASE CEL6A (FORMERLY CALLED CBH II)
KeywordsHYDROLASE / GLYCOSIDASE / GLYCOPROTEIN
Function / homology
Function and homology information


cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / cellulose binding / cellulose catabolic process / extracellular region / identical protein binding
Similarity search - Function
1, 4-beta cellobiohydrolase / Glycosyl hydrolases family 6 signature 2. / Glycosyl hydrolases family 6 signature 1. / Glycoside hydrolase, family 6, conserved site / 1, 4-beta cellobiohydrolase / 1, 4-beta cellobiohydrolase superfamily / Glycosyl hydrolases family 6 / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily ...1, 4-beta cellobiohydrolase / Glycosyl hydrolases family 6 signature 2. / Glycosyl hydrolases family 6 signature 1. / Glycoside hydrolase, family 6, conserved site / 1, 4-beta cellobiohydrolase / 1, 4-beta cellobiohydrolase superfamily / Glycosyl hydrolases family 6 / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / alpha-D-mannopyranose / Exoglucanase 2
Similarity search - Component
Biological speciesTRICHODERMA REESEI (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZou, J.-Y. / Jones, T.A.
Citation
Journal: Structure / Year: 1999
Title: Crystallographic Evidence for Substrate Ring Distortion and Protein Conformational Changes During Catalysis in Cellobiohydrolase Cel6A from Trichoderma Reesei
Authors: Zou, J.-Y. / Kleywegt, G.J. / Stahlberg, J. / Driguez, H. / Nerinckx, W. / Claeyssens, M. / Koivula, A. / Teeri, T.T. / Jones, T.A.
#1: Journal: Science / Year: 1990
Title: Three-Dimensional Structure of Cellobiohydrolase II from Trichoderma Reesei
Authors: Rouvinen, J. / Bergfors, T. / Teeri, T. / Knowles, J.K. / Jones, T.A.
History
DepositionJul 6, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 1999Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Oct 23, 2019Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Derived calculations / Experimental preparation / Other / Structure summary
Category: chem_comp / exptl_crystal_grow ...chem_comp / exptl_crystal_grow / pdbx_database_status / pdbx_entity_instance_feature / pdbx_entry_details / struct_conn
Item: _chem_comp.type / _exptl_crystal_grow.method ..._chem_comp.type / _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CELLOBIOHYDROLASE CEL6A (FORMERLY CALLED CBH II)
B: CELLOBIOHYDROLASE CEL6A (FORMERLY CALLED CBH II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,51328
Polymers78,0792
Non-polymers5,43426
Water13,187732
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A: CELLOBIOHYDROLASE CEL6A (FORMERLY CALLED CBH II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,75614
Polymers39,0391
Non-polymers2,71713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CELLOBIOHYDROLASE CEL6A (FORMERLY CALLED CBH II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,75614
Polymers39,0391
Non-polymers2,71713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)48.490, 74.310, 90.710
Angle α, β, γ (deg.)90.00, 103.82, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.999999, -0.001278, -0.000251), (0.001277, 0.999989, -0.00443), (0.000257, 0.004429, 0.99999)
Vector: -13.567, -48.691, -43.828)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CELLOBIOHYDROLASE CEL6A (FORMERLY CALLED CBH II) / CEL6A (Y169F)


Mass: 39039.297 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 83-447 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRICHODERMA REESEI (fungus) / Gene: CBH2 (Y169F) / Production host: TRICHODERMA REESEI (fungus)
References: UniProt: P07987, cellulose 1,4-beta-cellobiosidase (non-reducing end)

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Sugars , 3 types, 20 molecules

#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-methyl ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-methyl beta-D-glucopyranoside


Type: oligosaccharide / Mass: 696.669 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,4,3/[a2122h-1b_1-5_1*OC][a2122h-1b_1-5][a2122h-1a_1-5]/1-2-3-3/a4-b1_b4-c1*S*_c4-d1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-Glcp]{[(4+1)][b-D-Glcp4SH]{[(4+S)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 738 molecules

#5: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 732 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.48 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG6000, 20MM MES BUFFER PH6.0, 10MM CDCL2., pH 6.00
Crystal grow
*PLUS
Method: unknown / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 %PEG600011can be replaced by mPEG5000
220 mMMES11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Feb 15, 1996 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→47.1 Å / Num. obs: 44400 / % possible obs: 90.5 % / Redundancy: 2.3 % / Biso Wilson estimate: 11.1 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 17.3
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.094 / Mean I/σ(I) obs: 5.8 / % possible all: 64.3
Reflection shell
*PLUS
% possible obs: 64.3 %

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Processing

Software
NameVersionClassification
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED THE CATALYTIC CORE STARTS AT RESIDUE 83.
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1321 3 %RANDOM
Rwork0.179 ---
obs0.179 44348 90.1 %-
Solvent computationSolvent model: FLAT MODEL / ksol: 0.385127 e/Å3
Displacement parametersBiso mean: 11.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å21.02 Å2
2---0.61 Å20 Å2
3---1.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-20 Å
Luzzati sigma a0.16 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5478 0 318 732 6528
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.521.5
X-RAY DIFFRACTIONc_mcangle_it0.862
X-RAY DIFFRACTIONc_scbond_it0.872
X-RAY DIFFRACTIONc_scangle_it1.332.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.219 156 2.9 %
Rwork0.198 5276 -
obs--66.1 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

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